On Friday, 19 May 2017 at 22:53:39 UTC, crimaniak wrote:
On Friday, 19 May 2017 at 12:55:05 UTC, Biotronic wrote:
revComp6 seems to be the fastest, but it's probably also the
least readable (a common trade-off).
Try revComp7 with -release :)
string revComp7(string bps)
{
char[] result = new char[bps.length];
auto p1 = result.ptr;
auto p2 = &bps[$ - 1];
enum AT = 'A'^'T';
enum CG = 'C'^'G';
while (p2 > bps.ptr)
{
*p1 = *p2 ^ ((*p2 == 'A' || *p2 == 'T') ? AT : CG);
p1++;
p2--;
}
return result.assumeUnique;
}
In fact, when the size of the sequence is growing time
difference between procedures is shrinking, so it's much more
important to use memory-efficient presentation than to optimize
logic.
revComp7 is pretty fast, but I followed ag0aep6g's advice:
On Friday, 19 May 2017 at 13:38:20 UTC, ag0aep6g wrote:
Use `static immutable` instead. It still forces compile-time
calculation, but it doesn't have copy/paste behavior. Speeds up
revComp3 a lot.
Also, with DMD (2.073.0) -release -O instead of -debug from this
point. I'd blame someone else, but this is my fault. :p
Anyways, full collection of the various versions I've written,
plus crimaniak's revComp7 (rebranded as revComp8, because I
already had 7 at the time):
https://gist.github.com/Biotronic/20daaf0ed1262d313830bc8cd4199896
Timings:
revComp0: 158 ms, 926 us
revComp1: 1 sec, 157 ms, 15 us
revComp2: 604 ms, 37 us
revComp3: 18 ms, 545 us
revComp4: 92 ms, 293 us
revComp5: 86 ms, 731 us
revComp6: 94 ms, 56 us
revComp7: 917 ms, 576 us
revComp8: 62 ms, 917 us
This actually matches my expectations - the table lookup version
should be crazy fast, and it is. It beats even your revComp7
(revComp8 in the table).
LDC (-release -O3) timings:
revComp0: 166 ms, 190 us
revComp1: 352 ms, 917 us
revComp2: 300 ms, 493 us
revComp3: 10 ms, 950 us
revComp4: 148 ms, 106 us
revComp5: 144 ms, 152 us
revComp6: 142 ms, 307 us
revComp7: 604 ms, 274 us
revComp8: 26 ms, 612 us
Interesting how revComp4-6 got slower. What I really wanted to
see with this though, was the effect on revComp1, which uses
ranges all the way.
